Why we ask "Why?"
Asking why is often done because something in the question suggests that the person asking is going about solving their problem the wrong way. In those cases, oftentimes, the best way to answer the question is offer a different approach to the problem. Sometimes, though, there's a specific reason why a person has to approach the problem the way they have. We can't know that unless we get at least a basic understanding of why the asker is trying to do something a particular way, or what goal it is they're trying to accomplish. In other words, "why are you looking to do it this particular way?"
A good example of such a situation would be the common "how do I run a .exe file in Ubuntu?" The person answering has a couple of choices - answer the question as asked with no other questions ("use WINE"), answer it and offer what may be the better solution ("use WINE, but consider finding the Linux version"), or ask for clarification as to what application the person is trying to use ("oh, you want to run Chrome? Don't worry about the .exe, they have a native version. Using the native installer will save you the headache of trying to run it through WINE, which may or may not work as expected").
Some questions are, of course, easier to answer for both options, but some aren't - such as when answering the question, as asked, would result in the asker jumping through a number of unnecessary hoops in order to solve the issue in the manner they've started trying. In those cases, asking why can bring to light that they don't know of a different way (perhaps the documentation is outdated), and the answerer can show the asker a better way of getting to their goal.
Why comments sometimes seem rude
The StackExchange family of websites (of which AU is one) have been specifically groomed to not be "chatty." This is so ingrained, in fact, that the system itself works to enforce this by posting a "don't be chatty" line when a certain number of comments to a specific question or answer are reached, and enforcing character limits on comments. Things like greetings and signatures are also generally actively edited out of questions and answers.
Additionally, bluntness is encouraged. These are question and answer sites. People are here to get answers, not fuzzy feelings. That doesn't mean everything has to be robotic, but don't expect sugar-coating, either.
This does, however, mean that sometimes responses seem more abrasive than they actually are, especially if you're not already the type that's more inclined to such matter-of-fact responses, and if the response is directed at you.
fossfreedom's comment was not intentionally rude, he simply disagreed with your assessment that the comment was not constructive (which is subjective), nor was it spam (which is fairly objective). Since the comment is no longer present, I can't say either way whether I agree with his assessment, but I'm inclined to believe from your response here that it wasn't spam, but it may have been enough on the abrasive side to ruffle your feathers. Frankly, it happens to all of us at some point or another.
Why comments sometimes get deleted
Comments get deleted on a regular basis. I've seen whole strings of comments get deleted outright, and you can often see evidence of deleted comments in the responses that are left.
The most common reason is that they are "too chatty" or in general not very constructive. This is intended to keep things clean and in line with the things I mentioned earlier.
Occasionally, they do end up getting deleted because the conversation gets too heated. When that happens, the moderators will sometimes take more of a "scorched earth" approach, and delete all the comments involved in a particular discussion chain. This is to prevent the discussion from reigniting. It's all based on the circumstances of the conversation, though.
What to do with comments you don't like
There are a few things you can do with comments:
- Ignore them. They're just comments. (Though I have to say, sometimes I think it would be nice to be able to downvote comments.)
- Assume they weren't intentionally rude and answer the underlying question (ie - "why would you use encrypfs for everything?" would translate roughly into "your method seems like overkill and there are better ways, why did you choose to do it this way?" see again, my first point)
- Hop over to chat and ask someone for a second opinion
- Flag them. This is generally saved for comments that are intentionally inflammatory, rude, or spam. Also, just because you flag something (comment, question, or answer), it doesn't mean the moderators will agree with you. It's nothing personal.
This is just one of many example. I have seen this over and over and
freaking over again over SO. Is this is the price to pay for having
asked a Question here? Do have become a suspect for interrogation when
I ask a question on SO. Do we have to be punished by useless
questions, that bloat up the comments and help nobody but instead
wasting time of everybody?
I took the liberty of clicking through a few of the questions you've posted, and from what I saw, they were all quite civil. Now, I understand that they may (probably) have been cleaned up, but I can only judge by what I see, and between them and my own experiences with SE over the years, it seems to me that you may be overreacting somewhat. It's perfectly understandable, given that you just came from a bit of a ruffle (I felt the same way when I asked this question over on dba.SE and was met with what I felt to be a bitchy attitude, even by SE standards). Like I said earlier, though, it happens to all of us.
What I've found to help is to step away from it for a little while. If your question was sufficient enough for someone to take a stab at answering it, they probably will and the comment will either be rendered moot, or its point validated. If not, then you'll be able to answer the comment and re-read your question to provide clarification. If their tone still doesn't sit right with you, see if someone in chat can have a look and provide a different perspective. It's what I did with the question I linked. It was rough, but with the help of one of the mods, I was able to get the question worded properly so that a good answer could be written.